rs3829160

chr10-100355250-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005063.5(SCD):c.647+618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,056 control chromosomes in the GnomAD database, including 12,625 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (12625 hom., cov: 33)
• Consequence: SCD NM_005063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

SCD (HGNC:10571): (stearoyl-CoA desaturase) This gene encodes an enzyme involved in fatty acid biosynthesis, primarily the synthesis of oleic acid. The protein belongs to the fatty acid desaturase family and is an integral membrane protein located in the endoplasmic reticulum. Transcripts of approximately 3.9 and 5.2 kb, differing only by alternative polyadenlyation signals, have been detected. A gene encoding a similar enzyme is located on chromosome 4 and a pseudogene of this gene is located on chromosome 17. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCD	NM_005063.5	c.647+618G>A		intron_variant		ENST00000370355.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCD	ENST00000370355.3	c.647+618G>A		intron_variant		1	NM_005063.5	P1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57418 AN: 151938 Hom.: 12616 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.426

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.378 AC: 57438 AN: 152056 Hom.: 12625 Cov.: 33 AF XY: 0.375 AC XY: 27876 AN XY: 74310

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.424

Alfa AF: 0.443 Hom.: 3746

Bravo AF: 0.381

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.7
Dann	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3829160; hg19: chr10-102115007;